I am having the same issue. GoogleBot going crazy indexing the same PDFs over and over due to the random refresh parameter being added to the URL. I tried the Unmask Download Link and this did not remove the parameter. I also tried switching to a file uploaded to the WordPress Media library, this did not help. I then tried the Beta feature to activate flat download URL. For both the Download Manager and Media files I get a Page Not Found error. I have tested with the site cache off.Cleared my browser cache.Not sure where to go from here. I do not want to noindex the PDF downloads although may need to for now as Google is putting a significant load on the server from all of the downloading.